Determining how mega diverse microbial communities assemble in tropical rainforest canopies

Journal of Ecology has just published a new research article by Donald et al. “A test of community assembly rules using foliar endophytes from a tropical forest canopy

Authors Julian Donald, Léonie Péllissier and Uxue Suescun discuss how they used endophytes as a model system to test what factors best explain the assembly of diverse forest communities. They also reveal the fascinating logistics involved in collecting leaf samples from the upper canopies!


The diversity of species in tropical rainforests is nothing short of astounding. How can so many species live in one place when competing for a limited pool of resources? At the microscopic scale, the numbers of species co-occurring can be enough to make your head spin. Endophytic fungi and bacteria inhabit the leaves of plants without provoking symptomatic responses from their hosts, all the while benefiting from the resources contained within.

Studies using DNA-based methods have shown that in tropical forests, hundreds of different species can co-occur in a single leaf! This is even more incredible when you begin to consider the number of leaves in a single tree crown. Such a high number of individual organisms is likely to play an important role in plant host functioning, in particular in the most photosynthetically active layer of the upper canopy.

The upper canopy of a rainforest. Photo: Uxue Suescun

Given their organisation into discrete communities within each leaf, foliar endophytes provide an ideal model system to test what factors best explain the assembly of diverse communities in tropical forests. By determining how endophyte communities compare across individual branches, trees, and a range of host tree species, we can explore the role of dispersal limitation and niche specific factors. All of this of course, depends on being able to access the upper canopy in the first place…

Climbing the COPAS. Photo: Uxue Suescun

To get around this tricky issue, we used the ‘Canopy Operational Permanent Access System’ (COPAS) at the Nouragues Ecological Research Station in French Guiana, consisting of a trio of 45 m high pylons, linked by a system of Kevlar wires and a mechanically operated harness set up above a fully inventoried 4-h forest plot. We collected over 400 canopy top leaves from 31 individual trees belonging to 22 different species. These were then taken back to the lab where they were processed to extract the DNA contained within. DNA was subsequently amplified and sequenced, before bioinformatic processing to generate lists of the fungal and bacterial species found in each leaf (in this case Operational Taxonomic Units, OTUs).

Jerome returns with his harvest. Photo: Léonie Péllisier

By comparing species across sampling units, we were able to determine how the overall community structure changed from leaf to leaf, branch to branch, tree to tree and species to species. We could also see how communities changed as trees were further apart within the forest matrix. Overall, our study showed that whilst small amounts of community variation could be explained by distance between leaves in the canopy at the branch scale, that beyond this communities were much more likely to be structured randomly. Similarly, whilst communities of endophytes collected from leaves belonging to the same species were more similar than others, suggesting niche specific effects, this only explained a small part of the overall variation within the system.

Processing leaves to extract their DNA. Photo: Uxue Suescun

The organisation of communities of endophytes the canopy leaves of plants allows us to test the theoretical rules of community ecology. In addition, they serve to demonstrate how much hidden diversity remains in tropical forest habitats, how little we understand about their functioning and how much we are set to lose with habitat conversion and transformation.

Sampling in the canopy. Photo: Léonie Péllisier

Julian Donald Evolution et Diversité Biologique, Université Toulouse, Toulouse, France
Léonie Péllissier School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
Uxue Suescun Evolution et Diversité Biologique, Université Toulouse, Toulouse, France


For more information on the study of biodiversity in French Guiana, please refer to the CEBA website: http://www.labex-ceba.fr/en/

For more information on the study of endophytes and their role within plant hosts, please visit the SECIL research project website: http://secil.obs-banyuls.fr/index.php/accueil.html


Read the full research paper in Journal of Ecology: A test of community assembly rules using foliar endophytes from a tropical forest canopy

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